[galaxy-commits] [galaxyproject/galaxy] 510290: Add example of regressed 16.04 behavior related to...

GitHub noreply at github.com
Thu Sep 22 15:21:39 EDT 2016


  Branch: refs/heads/master-toolshed
  Home:   https://github.com/galaxyproject/galaxy
  Commit: 510290feea4bb328566770b636f9f093d00e93b0
      https://github.com/galaxyproject/galaxy/commit/510290feea4bb328566770b636f9f093d00e93b0
  Author: John Chilton <jmchilton at gmail.com>
  Date:   2016-08-16 (Tue, 16 Aug 2016)

  Changed paths:
    A test/functional/tools/dbkey_output_action.xml
    M test/functional/tools/samples_tool_conf.xml

  Log Message:
  -----------
  Add example of regressed 16.04 behavior related to dbkey output actions.


  Commit: 88d02dba6e851f0f60758a575920f6e7b130e261
      https://github.com/galaxyproject/galaxy/commit/88d02dba6e851f0f60758a575920f6e7b130e261
  Author: John Chilton <jmchilton at gmail.com>
  Date:   2016-08-16 (Tue, 16 Aug 2016)

  Changed paths:
    M lib/galaxy/tools/actions/__init__.py

  Log Message:
  -----------
  Don't fill in a cheetah default if unavailable.

... in metadata hack from #961.


  Commit: 0110d5a05a4b1b357a3f321471fce1b2d4960e67
      https://github.com/galaxyproject/galaxy/commit/0110d5a05a4b1b357a3f321471fce1b2d4960e67
  Author: John Chilton <jmchilton at gmail.com>
  Date:   2016-08-16 (Tue, 16 Aug 2016)

  Changed paths:
    M test/functional/tools/dbkey_output_action.xml

  Log Message:
  -----------
  Add a test case to dbkey_output_action.xml.

Per @nsoranzo's template and suggestion.


  Commit: e06cf9a97802d4c6a2ab97d973a373675e68b751
      https://github.com/galaxyproject/galaxy/commit/e06cf9a97802d4c6a2ab97d973a373675e68b751
  Author: John Chilton <jmchilton at gmail.com>
  Date:   2016-08-16 (Tue, 16 Aug 2016)

  Changed paths:
    M lib/galaxy/util/template.py

  Log Message:
  -----------
  Add None check to fill_template...

... as requested by @nsoranzo.


  Commit: d1c58f7ab039cc457d7e3fc97857cd2c314c5e5c
      https://github.com/galaxyproject/galaxy/commit/d1c58f7ab039cc457d7e3fc97857cd2c314c5e5c
  Author: Marius van den Beek <m.vandenbeek at gmail.com>
  Date:   2016-08-17 (Wed, 17 Aug 2016)

  Changed paths:
    M lib/galaxy/tools/actions/__init__.py
    M lib/galaxy/util/template.py
    A test/functional/tools/dbkey_output_action.xml
    M test/functional/tools/samples_tool_conf.xml

  Log Message:
  -----------
  Merge pull request #2800 from jmchilton/dbkey_output_without_cond

[16.04] Fix dbkey problem discovered by @hrhotz


  Commit: bf9a15389ef32de5ef09cc35876cc17154cb5a5d
      https://github.com/galaxyproject/galaxy/commit/bf9a15389ef32de5ef09cc35876cc17154cb5a5d
  Author: carlfeberhard <carlfeberhard at gmail.com>
  Date:   2016-08-17 (Wed, 17 Aug 2016)

  Changed paths:
    M lib/galaxy/webapps/galaxy/api/history_contents.py
    M static/scripts/bundled/analysis.bundled.js
    M static/scripts/bundled/analysis.bundled.js.map
    M static/scripts/bundled/libs.bundled.js
    M static/scripts/bundled/libs.bundled.js.map

  Log Message:
  -----------
  API, history contents: allow 'source' in payload

In create, checks both kwd and payload for 'source' parameter when
creating a new hdca. This allows source to be passed in the body and
not query string.

This fixes the copy call in history-contents when copying an hdca
by drag and drop in the multi history view.


  Commit: c3d7ca8eef014eb019493dbf06c250c0a586b97c
      https://github.com/galaxyproject/galaxy/commit/c3d7ca8eef014eb019493dbf06c250c0a586b97c
  Author: Nate Coraor <nate at bx.psu.edu>
  Date:   2016-08-17 (Wed, 17 Aug 2016)

  Changed paths:
    M lib/galaxy/jobs/runners/slurm.py

  Log Message:
  -----------
  Revert str.split() syntax for Python 2 compatibility


  Commit: 30d5b45d43c483c12390900a43d13fc9cb6667d5
      https://github.com/galaxyproject/galaxy/commit/30d5b45d43c483c12390900a43d13fc9cb6667d5
  Author: Dannon Baker <dannon.baker at gmail.com>
  Date:   2016-08-17 (Wed, 17 Aug 2016)

  Changed paths:
    M lib/galaxy/jobs/runners/slurm.py

  Log Message:
  -----------
  Merge pull request #2810 from natefoo/split-kwargs

[16.07] Revert str.split() syntax for Python 2 compatibility


  Commit: 6c2468832bdfbfa470596d2ae86f48dc54285139
      https://github.com/galaxyproject/galaxy/commit/6c2468832bdfbfa470596d2ae86f48dc54285139
  Author: Martin Cech <cech.marten at gmail.com>
  Date:   2016-08-17 (Wed, 17 Aug 2016)

  Changed paths:
    M lib/galaxy/webapps/galaxy/api/history_contents.py
    M static/scripts/bundled/analysis.bundled.js
    M static/scripts/bundled/analysis.bundled.js.map
    M static/scripts/bundled/libs.bundled.js
    M static/scripts/bundled/libs.bundled.js.map

  Log Message:
  -----------
  Merge pull request #2809 from carlfeberhard/fix.hdca-dnd

[16.07] API, history contents: allow 'source' in payload


  Commit: 1f69bf32e8cf3c073804d2cdbb3823e14f1a8ce5
      https://github.com/galaxyproject/galaxy/commit/1f69bf32e8cf3c073804d2cdbb3823e14f1a8ce5
  Author: Nicola Soranzo <nicola.soranzo at tgac.ac.uk>
  Date:   2016-08-18 (Thu, 18 Aug 2016)

  Changed paths:
    M run.sh

  Log Message:
  -----------
  Fix run.sh --daemon

Broken in commit d5c52cadfd0007338d4c89f505ff272e9acae9f9 .
Partial backport from #2765 .
Close #2724.


  Commit: a134587c893f6afa6f8bab1e9df7ff4ef74fa29c
      https://github.com/galaxyproject/galaxy/commit/a134587c893f6afa6f8bab1e9df7ff4ef74fa29c
  Author: Dave Bouvier <dave at bx.psu.edu>
  Date:   2016-08-18 (Thu, 18 Aug 2016)

  Changed paths:
    M lib/tool_shed/util/shed_util_common.py

  Log Message:
  -----------
  Correctly check set_environment declarations when updating repository.


  Commit: 3492e96574eabe6d2278cb294e9fdc0fe40b283c
      https://github.com/galaxyproject/galaxy/commit/3492e96574eabe6d2278cb294e9fdc0fe40b283c
  Author: Martin Cech <cech.marten at gmail.com>
  Date:   2016-08-18 (Thu, 18 Aug 2016)

  Changed paths:
    M lib/tool_shed/util/shed_util_common.py
    M run.sh

  Log Message:
  -----------
  Merge pull request #2811 from nsoranzo/release_16.04_backports

[16.04] Two backports


  Commit: f4806e9dd4b8b8f1743f9f081b00ef65029ea780
      https://github.com/galaxyproject/galaxy/commit/f4806e9dd4b8b8f1743f9f081b00ef65029ea780
  Author: Nicola Soranzo <nicola.soranzo at tgac.ac.uk>
  Date:   2016-08-18 (Thu, 18 Aug 2016)

  Changed paths:
    M lib/galaxy/tools/actions/__init__.py
    M lib/galaxy/util/template.py
    M run.sh
    A test/functional/tools/dbkey_output_action.xml
    M test/functional/tools/samples_tool_conf.xml

  Log Message:
  -----------
  Merge branch 'release_16.04' into release_16.07


  Commit: f47ea88c236be2414d40ef933dd3ee3c5aa2cbcb
      https://github.com/galaxyproject/galaxy/commit/f47ea88c236be2414d40ef933dd3ee3c5aa2cbcb
  Author: Martin Cech <cech.marten at gmail.com>
  Date:   2016-08-19 (Fri, 19 Aug 2016)

  Changed paths:
    A doc/source/releases/16.07.rst
    M doc/source/releases/16.07_announce.rst
    A doc/source/releases/16.10_announce.rst

  Log Message:
  -----------
  initial curated release notes for 16.07


  Commit: 873f34f07953eaf194ec0338139a736d413c30c0
      https://github.com/galaxyproject/galaxy/commit/873f34f07953eaf194ec0338139a736d413c30c0
  Author: Marius van den Beek <m.vandenbeek at gmail.com>
  Date:   2016-08-20 (Sat, 20 Aug 2016)

  Changed paths:
    M lib/galaxy/tools/deps/conda_util.py

  Log Message:
  -----------
  Inject HOME, so that conda doens't attempt to write to ~/.conda


  Commit: 53570e471e087fc92e0ef4befdd965703e4aeb14
      https://github.com/galaxyproject/galaxy/commit/53570e471e087fc92e0ef4befdd965703e4aeb14
  Author: Nicola Soranzo <nicola.soranzo at tgac.ac.uk>
  Date:   2016-08-22 (Mon, 22 Aug 2016)

  Changed paths:
    M doc/source/releases/16.07.rst

  Log Message:
  -----------
  Merge some entries, rephrasing and fixes


  Commit: 96bdde85bf259c2c821a7bbacc1c4aef60c3f3b7
      https://github.com/galaxyproject/galaxy/commit/96bdde85bf259c2c821a7bbacc1c4aef60c3f3b7
  Author: Martin Cech <cech.marten at gmail.com>
  Date:   2016-08-22 (Mon, 22 Aug 2016)

  Changed paths:
    M doc/source/releases/16.07_announce.rst

  Log Message:
  -----------
  add a highlight, update git commands


  Commit: 113999e5d574b29e1c197bcfe1bdef1777c5c507
      https://github.com/galaxyproject/galaxy/commit/113999e5d574b29e1c197bcfe1bdef1777c5c507
  Author: John Chilton <jmchilton at gmail.com>
  Date:   2016-08-22 (Mon, 22 Aug 2016)

  Changed paths:
    M doc/source/releases/16.07.rst

  Log Message:
  -----------
  Tweaks to language of many of enhancements in 16.07 release notes.


  Commit: c82719f22d3d8971055fc9b833dc7fd2519fad22
      https://github.com/galaxyproject/galaxy/commit/c82719f22d3d8971055fc9b833dc7fd2519fad22
  Author: Martin Cech <cech.marten at gmail.com>
  Date:   2016-08-22 (Mon, 22 Aug 2016)

  Changed paths:
    M doc/source/releases/16.07.rst
    M doc/source/releases/16.07_announce.rst

  Log Message:
  -----------
  drop subheaders, reorder, tweak to wording


  Commit: 9b96d9dbfa875375bc172451fb9c7e6993c62f41
      https://github.com/galaxyproject/galaxy/commit/9b96d9dbfa875375bc172451fb9c7e6993c62f41
  Author: John Chilton <jmchilton at gmail.com>
  Date:   2016-08-22 (Mon, 22 Aug 2016)

  Changed paths:
    M doc/source/releases/16.07.rst

  Log Message:
  -----------
  More user-focused language in release notes.


  Commit: e1060bd18fcf1bc69e5cd41f44adde37ba55ae1d
      https://github.com/galaxyproject/galaxy/commit/e1060bd18fcf1bc69e5cd41f44adde37ba55ae1d
  Author: John Chilton <jmchilton at gmail.com>
  Date:   2016-08-22 (Mon, 22 Aug 2016)

  Changed paths:
    M doc/source/releases/16.07.rst

  Log Message:
  -----------
  Spelling fix thanks to @nsoranzo.


  Commit: 04370845451da1cf839d75366d131325105698fe
      https://github.com/galaxyproject/galaxy/commit/04370845451da1cf839d75366d131325105698fe
  Author: John Chilton <jmchilton at gmail.com>
  Date:   2016-08-22 (Mon, 22 Aug 2016)

  Changed paths:
    M doc/source/releases/16.07.rst

  Log Message:
  -----------
  Another spelling fix thanks to @nsoranzo.


  Commit: 8f571bae7129b4ce07739ab8e4d9ddcef020af5e
      https://github.com/galaxyproject/galaxy/commit/8f571bae7129b4ce07739ab8e4d9ddcef020af5e
  Author: John Chilton <jmchilton at gmail.com>
  Date:   2016-08-22 (Mon, 22 Aug 2016)

  Changed paths:
    M doc/source/releases/16.07.rst

  Log Message:
  -----------
  Wording fix thanks to @nsoranzo.


  Commit: f0ffa9c5947674d8e8731f36f00eb82b757b6558
      https://github.com/galaxyproject/galaxy/commit/f0ffa9c5947674d8e8731f36f00eb82b757b6558
  Author: Martin Cech <cech.marten at gmail.com>
  Date:   2016-08-22 (Mon, 22 Aug 2016)

  Changed paths:
    M doc/source/releases/16.07.rst

  Log Message:
  -----------
  drop GRT reference


  Commit: 3d4300e5429b2b09b92cf5d9f55541643a0ff62b
      https://github.com/galaxyproject/galaxy/commit/3d4300e5429b2b09b92cf5d9f55541643a0ff62b
  Author: Martin Cech <cech.marten at gmail.com>
  Date:   2016-08-22 (Mon, 22 Aug 2016)

  Changed paths:
    M doc/source/releases/16.07.rst

  Log Message:
  -----------
  tweak wording of notes


  Commit: 26ceef668c57c0ef44f4072d3550472ff9582e29
      https://github.com/galaxyproject/galaxy/commit/26ceef668c57c0ef44f4072d3550472ff9582e29
  Author: Martin Cech <cech.marten at gmail.com>
  Date:   2016-08-22 (Mon, 22 Aug 2016)

  Changed paths:
    M doc/source/releases/16.07_announce.rst

  Log Message:
  -----------
  announce conda as beta, link the IUC doc, link DTD wiki


  Commit: c33bf2a222a09cc7707bdf621c257e1a951f969a
      https://github.com/galaxyproject/galaxy/commit/c33bf2a222a09cc7707bdf621c257e1a951f969a
  Author: Marius van den Beek <m.vandenbeek at gmail.com>
  Date:   2016-08-23 (Tue, 23 Aug 2016)

  Changed paths:
    M lib/galaxy/tools/deps/conda_util.py

  Log Message:
  -----------
  Merge pull request #2825 from mvdbeek/conda_install_fix

Inject HOME, so that conda doens't attempt to write to ~/.conda


  Commit: c6c646ead407ef29a42ff6a6de7182837a97a1f7
      https://github.com/galaxyproject/galaxy/commit/c6c646ead407ef29a42ff6a6de7182837a97a1f7
  Author: Eric Rasche <rasche.eric at gmail.com>
  Date:   2016-08-23 (Tue, 23 Aug 2016)

  Changed paths:
    A doc/source/admin/chat-0.png
    A doc/source/admin/chat-1.png
    A doc/source/admin/chat-2.png
    A doc/source/admin/chat-3.png
    A doc/source/admin/chat-4.png
    A doc/source/admin/chat.rst
    A doc/source/admin/communication_server.png
    A doc/source/admin/communication_server_rooms.png
    M doc/source/admin/index.rst

  Log Message:
  -----------
  Document the Chat Server


  Commit: a1b2ec386e32f9fc357cb86836033a46084d8855
      https://github.com/galaxyproject/galaxy/commit/a1b2ec386e32f9fc357cb86836033a46084d8855
  Author: Martin Cech <cech.marten at gmail.com>
  Date:   2016-08-23 (Tue, 23 Aug 2016)

  Changed paths:
    A doc/source/admin/chat-0.png
    A doc/source/admin/chat-1.png
    A doc/source/admin/chat-2.png
    A doc/source/admin/chat-3.png
    A doc/source/admin/chat-4.png
    A doc/source/admin/chat.rst
    A doc/source/admin/communication_server.png
    A doc/source/admin/communication_server_rooms.png
    M doc/source/admin/index.rst

  Log Message:
  -----------
  Merge pull request #2843 from erasche/chat-docs

[16.07] Document the Chat Server


  Commit: 4d19755c1313e8a014f873f1b011baf4f8d59310
      https://github.com/galaxyproject/galaxy/commit/4d19755c1313e8a014f873f1b011baf4f8d59310
  Author: Martin Cech <cech.marten at gmail.com>
  Date:   2016-08-23 (Tue, 23 Aug 2016)

  Changed paths:
    A doc/source/admin/conda_faq.rst
    M doc/source/admin/index.rst

  Log Message:
  -----------
  add conda docs converted and modified from IUC googledoc


  Commit: 01a24f6560be2d6cc9c6aef43e9665f140fc3640
      https://github.com/galaxyproject/galaxy/commit/01a24f6560be2d6cc9c6aef43e9665f140fc3640
  Author: Martin Cech <cech.marten at gmail.com>
  Date:   2016-08-23 (Tue, 23 Aug 2016)

  Changed paths:
    M doc/source/admin/conda_faq.rst

  Log Message:
  -----------
  rst problems


  Commit: 04f22b70a4ecd127e7990982c09db7278bf1cf98
      https://github.com/galaxyproject/galaxy/commit/04f22b70a4ecd127e7990982c09db7278bf1cf98
  Author: Martin Cech <cech.marten at gmail.com>
  Date:   2016-08-23 (Tue, 23 Aug 2016)

  Changed paths:
    M doc/source/admin/conda_faq.rst

  Log Message:
  -----------
  fix plural, split lines to prevent indentation


  Commit: e33f8fe5b623d38ec7b27c90279713a18807ee48
      https://github.com/galaxyproject/galaxy/commit/e33f8fe5b623d38ec7b27c90279713a18807ee48
  Author: Martin Cech <cech.marten at gmail.com>
  Date:   2016-08-23 (Tue, 23 Aug 2016)

  Changed paths:
    M doc/source/admin/conda_faq.rst

  Log Message:
  -----------
  replace apostrophes


  Commit: 453c98d8ad572b7d9154430f5f61123d7ca5fbc4
      https://github.com/galaxyproject/galaxy/commit/453c98d8ad572b7d9154430f5f61123d7ca5fbc4
  Author: Martin Cech <cech.marten at gmail.com>
  Date:   2016-08-23 (Tue, 23 Aug 2016)

  Changed paths:
    M doc/source/admin/conda_faq.rst

  Log Message:
  -----------
  this one is even weirder than the ones before


  Commit: aedfdffafedd35a1ed52aec85dd373c76b7c3135
      https://github.com/galaxyproject/galaxy/commit/aedfdffafedd35a1ed52aec85dd373c76b7c3135
  Author: Martin Cech <cech.marten at gmail.com>
  Date:   2016-08-23 (Tue, 23 Aug 2016)

  Changed paths:
    M doc/source/admin/conda_faq.rst

  Log Message:
  -----------
  add more literal includes


  Commit: e52dbde3e481a30c5980f1e0171b720c557ee72d
      https://github.com/galaxyproject/galaxy/commit/e52dbde3e481a30c5980f1e0171b720c557ee72d
  Author: Dannon Baker <dannon.baker at gmail.com>
  Date:   2016-08-23 (Tue, 23 Aug 2016)

  Changed paths:
    M doc/source/admin/conda_faq.rst

  Log Message:
  -----------
  Conda/conda standardization


  Commit: b4495c1a8bb3e184bf35a9ebc4e795b7da3aadbb
      https://github.com/galaxyproject/galaxy/commit/b4495c1a8bb3e184bf35a9ebc4e795b7da3aadbb
  Author: Martin Cech <cech.marten at gmail.com>
  Date:   2016-08-23 (Tue, 23 Aug 2016)

  Changed paths:
    M doc/source/admin/conda_faq.rst

  Log Message:
  -----------
  Merge pull request #17 from dannon/docs_conda

Conda/conda standardization


  Commit: 3d0bf645ab03585e316d673cd6b073e706fb616d
      https://github.com/galaxyproject/galaxy/commit/3d0bf645ab03585e316d673cd6b073e706fb616d
  Author: Martin Cech <cech.marten at gmail.com>
  Date:   2016-08-24 (Wed, 24 Aug 2016)

  Changed paths:
    M doc/source/admin/conda_faq.rst

  Log Message:
  -----------
  fix tiny things in docs


  Commit: 779c357dcac2940f9bdaacf8de5259fe632ada1c
      https://github.com/galaxyproject/galaxy/commit/779c357dcac2940f9bdaacf8de5259fe632ada1c
  Author: Martin Cech <cech.marten at gmail.com>
  Date:   2016-08-24 (Wed, 24 Aug 2016)

  Changed paths:
    M doc/source/admin/conda_faq.rst

  Log Message:
  -----------
  Merge branch 'docs_conda' of https://github.com/martenson/galaxy into docs_conda


  Commit: 124d546be6e789a288f19c21adb229e149e9d7d2
      https://github.com/galaxyproject/galaxy/commit/124d546be6e789a288f19c21adb229e149e9d7d2
  Author: Dannon Baker <dannon.baker at gmail.com>
  Date:   2016-08-24 (Wed, 24 Aug 2016)

  Changed paths:
    A doc/source/admin/conda_faq.rst
    M doc/source/admin/index.rst

  Log Message:
  -----------
  Merge pull request #2844 from martenson/docs_conda

[16.07] add conda docs converted and modified from IUC googledoc


  Commit: 7326498335804560d0376c555524b096c69720ce
      https://github.com/galaxyproject/galaxy/commit/7326498335804560d0376c555524b096c69720ce
  Author: Martin Cech <cech.marten at gmail.com>
  Date:   2016-08-24 (Wed, 24 Aug 2016)

  Changed paths:
    M doc/source/admin/conda_faq.rst

  Log Message:
  -----------
  improve conda doc to include TOC


  Commit: 08b2bda13bd4622d9e492aaa256d7c9bba5790aa
      https://github.com/galaxyproject/galaxy/commit/08b2bda13bd4622d9e492aaa256d7c9bba5790aa
  Author: Martin Cech <cech.marten at gmail.com>
  Date:   2016-08-24 (Wed, 24 Aug 2016)

  Changed paths:
    M doc/source/releases/16.07_announce.rst

  Log Message:
  -----------
  change links to target official docs


  Commit: df47bd2007365f22921375fd0eb757f0ec749473
      https://github.com/galaxyproject/galaxy/commit/df47bd2007365f22921375fd0eb757f0ec749473
  Author: John Chilton <jmchilton at gmail.com>
  Date:   2016-08-24 (Wed, 24 Aug 2016)

  Changed paths:
    A doc/source/releases/16.07.rst
    M doc/source/releases/16.07_announce.rst
    A doc/source/releases/16.10_announce.rst

  Log Message:
  -----------
  Merge pull request #2821 from martenson/16.07_release_notes

[16.07] curated release notes for 16.07


  Commit: 3248b679ac91fbb2275fd3cd47d2fb2ea96e5a2e
      https://github.com/galaxyproject/galaxy/commit/3248b679ac91fbb2275fd3cd47d2fb2ea96e5a2e
  Author: John Chilton <jmchilton at gmail.com>
  Date:   2016-08-24 (Wed, 24 Aug 2016)

  Changed paths:
    M doc/source/admin/conda_faq.rst

  Log Message:
  -----------
  Merge pull request #2850 from martenson/docs_conda

[16.07] conda docs - add TOC


  Commit: 8b67ddfa37f82081791bcca5330983a2dd1301f9
      https://github.com/galaxyproject/galaxy/commit/8b67ddfa37f82081791bcca5330983a2dd1301f9
  Author: Marius van den Beek <m.vandenbeek at gmail.com>
  Date:   2016-08-24 (Wed, 24 Aug 2016)

  Changed paths:
    M lib/galaxy/tools/deps/resolvers/conda.py

  Log Message:
  -----------
  Acquire lock before attempting to install conda


  Commit: a2f234d5661f88263e1e6c5e8edef1e521b55359
      https://github.com/galaxyproject/galaxy/commit/a2f234d5661f88263e1e6c5e8edef1e521b55359
  Author: Marius van den Beek <m.vandenbeek at gmail.com>
  Date:   2016-08-24 (Wed, 24 Aug 2016)

  Changed paths:
    M lib/galaxy/tools/deps/resolvers/conda.py

  Log Message:
  -----------
  Create default tool_dependency dir if it doesn't exist


  Commit: e9d81500caa3526200b204270aca175839f36f56
      https://github.com/galaxyproject/galaxy/commit/e9d81500caa3526200b204270aca175839f36f56
  Author: Bjoern Gruening <bjoern.gruening at gmail.com>
  Date:   2016-08-24 (Wed, 24 Aug 2016)

  Changed paths:
    M lib/galaxy/tools/deps/conda_util.py

  Log Message:
  -----------
  shorten Conda environment names


  Commit: fad13d50c344112c8ab637e3c568e43d863730bd
      https://github.com/galaxyproject/galaxy/commit/fad13d50c344112c8ab637e3c568e43d863730bd
  Author: John Chilton <jmchilton at gmail.com>
  Date:   2016-08-24 (Wed, 24 Aug 2016)

  Changed paths:
    M lib/galaxy/tools/deps/conda_util.py
    M lib/galaxy/tools/deps/resolvers/conda.py

  Log Message:
  -----------
  Merge pull request #2851 from martenson/backport_2794_2826

[16.07] Backport conda fixes


  Commit: e5a1cabe8e4268813bf20156690202973fb07207
      https://github.com/galaxyproject/galaxy/commit/e5a1cabe8e4268813bf20156690202973fb07207
  Author: Martin Cech <cech.marten at gmail.com>
  Date:   2016-08-25 (Thu, 25 Aug 2016)

  Changed paths:
    M templates/webapps/tool_shed/index.mako

  Log Message:
  -----------
  unicodify time on shed counter

to prevent problems with dates that contain non-ascii


  Commit: 992cd51ac3aaa284478813196ef8aa0cb2c16246
      https://github.com/galaxyproject/galaxy/commit/992cd51ac3aaa284478813196ef8aa0cb2c16246
  Author: John Chilton <jmchilton at gmail.com>
  Date:   2016-08-25 (Thu, 25 Aug 2016)

  Changed paths:
    M templates/webapps/tool_shed/index.mako

  Log Message:
  -----------
  Merge pull request #2855 from martenson/fix-ts-unicodify

[16.07] unicodify TS main template


  Commit: 4f3c44f3ad386a667f156f39d1af44bf23b7a8ab
      https://github.com/galaxyproject/galaxy/commit/4f3c44f3ad386a667f156f39d1af44bf23b7a8ab
  Author: Nate Coraor <nate at bx.psu.edu>
  Date:   2016-08-25 (Thu, 25 Aug 2016)

  Changed paths:
    M lib/galaxy/tools/toolbox/base.py
    M lib/galaxy/tools/toolbox/watcher.py

  Log Message:
  -----------
  Move the registration of the start function into the ToolConfWatcher
itself so it doesn't have to be called by things that instantiate it.
Fixes #2831.


  Commit: e0aad7af47547c04013dffe3874e757c905b2021
      https://github.com/galaxyproject/galaxy/commit/e0aad7af47547c04013dffe3874e757c905b2021
  Author: John Chilton <jmchilton at gmail.com>
  Date:   2016-08-25 (Thu, 25 Aug 2016)

  Changed paths:
    M lib/galaxy/version.py

  Log Message:
  -----------
  Update version to 16.07


  Commit: 6631367b7cd4f2049426f3554eef6da626b83837
      https://github.com/galaxyproject/galaxy/commit/6631367b7cd4f2049426f3554eef6da626b83837
  Author: Dannon Baker <dannon.baker at gmail.com>
  Date:   2016-08-25 (Thu, 25 Aug 2016)

  Changed paths:
    M lib/galaxy/tools/toolbox/base.py

  Log Message:
  -----------
  Unused import, cleanup for #2856


  Commit: 3e65a165b722740b48ece5dab36a2a28cfa7681c
      https://github.com/galaxyproject/galaxy/commit/3e65a165b722740b48ece5dab36a2a28cfa7681c
  Author: Martin Cech <cech.marten at gmail.com>
  Date:   2016-08-25 (Thu, 25 Aug 2016)

  Changed paths:
    M doc/source/releases/16.07.rst

  Log Message:
  -----------
  fix inclusion of release notes in announcement


  Commit: c98331eddd3f8a57cedca313249798e1e45a9555
      https://github.com/galaxyproject/galaxy/commit/c98331eddd3f8a57cedca313249798e1e45a9555
  Author: Martin Cech <cech.marten at gmail.com>
  Date:   2016-08-25 (Thu, 25 Aug 2016)

  Changed paths:
    M lib/galaxy/tools/toolbox/base.py
    M lib/galaxy/tools/toolbox/watcher.py

  Log Message:
  -----------
  Merge pull request #2856 from natefoo/postfork-tool-conf-watcher-test-fix

[16.07] Postfork tool conf watcher test fix


  Commit: 53a5b76ff2e47bbf821845e0d2170240902a70eb
      https://github.com/galaxyproject/galaxy/commit/53a5b76ff2e47bbf821845e0d2170240902a70eb
  Author: Martin Cech <cech.marten at gmail.com>
  Date:   2016-08-25 (Thu, 25 Aug 2016)

  Changed paths:
    M lib/galaxy/tools/toolbox/base.py

  Log Message:
  -----------
  Merge pull request #2860 from dannon/postfork-tool-conf-watcher-test-fix

[16.07] Unused import cleanup for #2856


  Commit: e891c5755f59e8865cbee56cd4fcc8e5f4bbd0af
      https://github.com/galaxyproject/galaxy/commit/e891c5755f59e8865cbee56cd4fcc8e5f4bbd0af
  Author: Dannon Baker <dannon.baker at gmail.com>
  Date:   2016-08-25 (Thu, 25 Aug 2016)

  Changed paths:
    M doc/source/releases/16.07.rst

  Log Message:
  -----------
  Merge pull request #2859 from martenson/fix-notes-include

[16.07] fix inclusion of release notes in the announcement


  Commit: d1821fed475a4261c007de3627cb3eeb42d53a1f
      https://github.com/galaxyproject/galaxy/commit/d1821fed475a4261c007de3627cb3eeb42d53a1f
  Author: Martin Cech <cech.marten at gmail.com>
  Date:   2016-08-26 (Fri, 26 Aug 2016)

  Changed paths:
    M config/galaxy.ini.sample
    M lib/galaxy/tools/deps/__init__.py

  Log Message:
  -----------
  disable conda_auto_init


  Commit: 52768c0c42313c08f25ba07b47ccf2bed28248f4
      https://github.com/galaxyproject/galaxy/commit/52768c0c42313c08f25ba07b47ccf2bed28248f4
  Author: Dannon Baker <dannon.baker at gmail.com>
  Date:   2016-08-26 (Fri, 26 Aug 2016)

  Changed paths:
    M config/galaxy.ini.sample
    M lib/galaxy/tools/deps/__init__.py

  Log Message:
  -----------
  Merge pull request #2863 from martenson/release_16.07

[16.07] backport disable conda_auto_init


  Commit: 6724146e7d09e5c0ac4f19d96e600d14831a8abe
      https://github.com/galaxyproject/galaxy/commit/6724146e7d09e5c0ac4f19d96e600d14831a8abe
  Author: John Chilton <jmchilton at gmail.com>
  Date:   2016-08-26 (Fri, 26 Aug 2016)

  Changed paths:
    M lib/galaxy/tools/deps/resolvers/conda.py

  Log Message:
  -----------
  Fix three conda bugs.

- Don't attempt file lock if don't have write access for lock.
- Set disabled to False if conda present and auto_init is False.
- Use the correct parent path for conda_prefix (if default parent path is overridden).


  Commit: c01ce21e2cdb7b229dd8ced14e4e2c1c7fdf294c
      https://github.com/galaxyproject/galaxy/commit/c01ce21e2cdb7b229dd8ced14e4e2c1c7fdf294c
  Author: Martin Cech <cech.marten at gmail.com>
  Date:   2016-08-26 (Fri, 26 Aug 2016)

  Changed paths:
    M lib/galaxy/tools/deps/resolvers/conda.py

  Log Message:
  -----------
  Merge pull request #2864 from jmchilton/conda_fixes

[16.07] Fix three conda bugs.


  Commit: 91a190c6eb2f37e041575548bfae85d61b64ce7e
      https://github.com/galaxyproject/galaxy/commit/91a190c6eb2f37e041575548bfae85d61b64ce7e
  Author: carlfeberhard <carlfeberhard at gmail.com>
  Date:   2016-09-12 (Mon, 12 Sep 2016)

  Changed paths:
    M lib/galaxy/managers/datasets.py
    M test/unit/managers/test_DatasetManager.py

  Log Message:
  -----------
  Datasets: allow admin to serialize permissions

And updates tests.


  Commit: b88035955d7a81ff43858f092924b60bef1bca9c
      https://github.com/galaxyproject/galaxy/commit/b88035955d7a81ff43858f092924b60bef1bca9c
  Author: carlfeberhard <carlfeberhard at gmail.com>
  Date:   2016-09-12 (Mon, 12 Sep 2016)

  Changed paths:
    M test/unit/managers/test_DatasetManager.py

  Log Message:
  -----------
  Datasets: confirm admin ability to set permissions

The power was inside you all along.


  Commit: 8616c0e87c055ed8e41563625498818a76769b2f
      https://github.com/galaxyproject/galaxy/commit/8616c0e87c055ed8e41563625498818a76769b2f
  Author: Marius van den Beek <m.vandenbeek at gmail.com>
  Date:   2016-09-13 (Tue, 13 Sep 2016)

  Changed paths:
    M lib/galaxy/tools/deps/__init__.py
    M lib/galaxy/tools/deps/resolvers/__init__.py

  Log Message:
  -----------
  Log the resolved dependency type


  Commit: fc3dcf3b875cbadf75a1eb34ce1395e29dbe0baf
      https://github.com/galaxyproject/galaxy/commit/fc3dcf3b875cbadf75a1eb34ce1395e29dbe0baf
  Author: carlfeberhard <carlfeberhard at gmail.com>
  Date:   2016-09-13 (Tue, 13 Sep 2016)

  Changed paths:
    M lib/galaxy/managers/datasets.py
    M lib/galaxy/managers/rbac_secured.py
    M test/unit/managers/test_DatasetManager.py

  Log Message:
  -----------
  Permissions, datasets: allow admin in RBAC

- Admin are considered permitted when calling
  ** dataset_manager.permssions.access and
  ** dataset_manager.permissions.manage
- Update bad test
- Add admin test to other permission checks


  Commit: 9636ea1b6cb1283ef9e5d8cb210a962eff45bbef
      https://github.com/galaxyproject/galaxy/commit/9636ea1b6cb1283ef9e5d8cb210a962eff45bbef
  Author: carlfeberhard <carlfeberhard at gmail.com>
  Date:   2016-09-13 (Tue, 13 Sep 2016)

  Changed paths:
    M test/unit/managers/test_DatasetManager.py

  Log Message:
  -----------
  Datasets: test for anon access/manage


  Commit: e7cb0ac2a19f0141336285fdd8fcf9aeb32221f2
      https://github.com/galaxyproject/galaxy/commit/e7cb0ac2a19f0141336285fdd8fcf9aeb32221f2
  Author: carlfeberhard <carlfeberhard at gmail.com>
  Date:   2016-09-13 (Tue, 13 Sep 2016)

  Changed paths:
    M test/unit/managers/test_DatasetManager.py

  Log Message:
  -----------
  Datasets: test for anon deserialization


  Commit: b301fd42021245f5c3c7291207510659aa66b5ac
      https://github.com/galaxyproject/galaxy/commit/b301fd42021245f5c3c7291207510659aa66b5ac
  Author: carlfeberhard <carlfeberhard at gmail.com>
  Date:   2016-09-14 (Wed, 14 Sep 2016)

  Changed paths:
    M lib/galaxy/managers/rbac_secured.py

  Log Message:
  -----------
  Dataset perms: correct comment


  Commit: 8bf7256ca8ec61a167bca1dcaafa0b83cf12fa5a
      https://github.com/galaxyproject/galaxy/commit/8bf7256ca8ec61a167bca1dcaafa0b83cf12fa5a
  Author: Martin Cech <cech.marten at gmail.com>
  Date:   2016-09-14 (Wed, 14 Sep 2016)

  Changed paths:
    M lib/galaxy/managers/rbac_secured.py
    M test/unit/managers/test_DatasetManager.py

  Log Message:
  -----------
  Merge pull request #2912 from carlfeberhard/dataset.admin-permissions

[16.01] Allow admin to serialize/deserialize dataset permissions


  Commit: b50d07d5bf128ee280eb823f9b2b5677e549b5e5
      https://github.com/galaxyproject/galaxy/commit/b50d07d5bf128ee280eb823f9b2b5677e549b5e5
  Author: carlfeberhard <carlfeberhard at gmail.com>
  Date:   2016-09-14 (Wed, 14 Sep 2016)

  Changed paths:
    M lib/galaxy/managers/rbac_secured.py
    M test/unit/managers/test_DatasetManager.py

  Log Message:
  -----------
  Merge remote-tracking branch 'upstream/release_16.01' into release_16.04


  Commit: e5f4f2fab6ce44b4e98f1dc54bea138d1185aa85
      https://github.com/galaxyproject/galaxy/commit/e5f4f2fab6ce44b4e98f1dc54bea138d1185aa85
  Author: carlfeberhard <carlfeberhard at gmail.com>
  Date:   2016-09-14 (Wed, 14 Sep 2016)

  Changed paths:
    M lib/galaxy/managers/rbac_secured.py
    M test/unit/managers/test_DatasetManager.py

  Log Message:
  -----------
  Merge remote-tracking branch 'upstream/release_16.04' into release_16.07


  Commit: 646428d73f9cbcd312ed3ff5eff8e36ee12f213e
      https://github.com/galaxyproject/galaxy/commit/646428d73f9cbcd312ed3ff5eff8e36ee12f213e
  Author: guerler <aysam.guerler at gmail.com>
  Date:   2016-09-14 (Wed, 14 Sep 2016)

  Changed paths:
    M templates/webapps/galaxy/workflow/run.mako

  Log Message:
  -----------
  Remove change handler for data and collection multiinput selectors in old run workflow form


  Commit: b399c086254f35d8536c1afa9fd7a2e50ec339a9
      https://github.com/galaxyproject/galaxy/commit/b399c086254f35d8536c1afa9fd7a2e50ec339a9
  Author: John Chilton <jmchilton at gmail.com>
  Date:   2016-09-14 (Wed, 14 Sep 2016)

  Changed paths:
    M lib/galaxy/tools/deps/__init__.py
    M lib/galaxy/tools/deps/resolvers/__init__.py

  Log Message:
  -----------
  Merge pull request #2918 from martenson/pick-dep-log

[16.07] cherry pick logging the resolved dependency type


  Commit: 67a3cf34ca0e639791ac88e849d120dce355d3ef
      https://github.com/galaxyproject/galaxy/commit/67a3cf34ca0e639791ac88e849d120dce355d3ef
  Author: Martin Cech <cech.marten at gmail.com>
  Date:   2016-09-15 (Thu, 15 Sep 2016)

  Changed paths:
    M templates/webapps/galaxy/workflow/run.mako

  Log Message:
  -----------
  Merge pull request #2920 from guerler/fix_collection_refresh

[16.07] Prevent refresh for collection selector in old run workflow form


  Commit: dc5aff7e44e2b0f767b7578935d46db7d7707066
      https://github.com/galaxyproject/galaxy/commit/dc5aff7e44e2b0f767b7578935d46db7d7707066
  Author: Anthony Bretaudeau <abretaud at irisa.fr>
  Date:   2016-09-15 (Thu, 15 Sep 2016)

  Changed paths:
    M lib/galaxy/dependencies/conditional-requirements.txt

  Log Message:
  -----------
  Update python-ldap module

Updating to the same version as galaxyproject/starforge#97


  Commit: c497ea534897b4c1875186961e96da52129c4a3a
      https://github.com/galaxyproject/galaxy/commit/c497ea534897b4c1875186961e96da52129c4a3a
  Author: Daniel Blankenberg <dan.blankenberg at gmail.com>
  Date:   2016-09-16 (Fri, 16 Sep 2016)

  Changed paths:
    M lib/galaxy/dependencies/conditional-requirements.txt

  Log Message:
  -----------
  Merge pull request #2924 from nsoranzo/release_16.07_backport_2738

[16.07] Update python-ldap module


  Commit: 1f53c32ad68235537d8f6c843d1cd81eda5c11c3
      https://github.com/galaxyproject/galaxy/commit/1f53c32ad68235537d8f6c843d1cd81eda5c11c3
  Author: Nicola Soranzo <nicola.soranzo at tgac.ac.uk>
  Date:   2016-09-19 (Mon, 19 Sep 2016)

  Changed paths:
    A lib/galaxy/datatypes/converters/tabular_to_dbnsfp.py

  Log Message:
  -----------
  Add missing tabular_to_dbnsfp.py for dbnsfp.tabular to snpsiftdbnsfp conversion

This should have been added in https://bitbucket.org/galaxy/galaxy-central/pull-requests/640/
Actual source code comes from https://github.com/galaxyproject/tools-iuc/blob/master/datatypes/snpsift_dbnsfp_datatypes/tabular_to_dbnsfp.py


  Commit: b748250193a26ddce4010759b9a22d012d281b81
      https://github.com/galaxyproject/galaxy/commit/b748250193a26ddce4010759b9a22d012d281b81
  Author: John Chilton <jmchilton at gmail.com>
  Date:   2016-09-20 (Tue, 20 Sep 2016)

  Changed paths:
    A lib/galaxy/datatypes/converters/tabular_to_dbnsfp.py

  Log Message:
  -----------
  Merge pull request #2938 from nsoranzo/release_16.04_tabular_to_dbnsfp

[16.04] Add missing tabular_to_dbnsfp.py for dbnsfp.tabular to snpsiftdbnsfp conversion


  Commit: 7627abb3856a4e757b5ed5c55ec05a4f97bd4cac
      https://github.com/galaxyproject/galaxy/commit/7627abb3856a4e757b5ed5c55ec05a4f97bd4cac
  Author: Nicola Soranzo <nicola.soranzo at tgac.ac.uk>
  Date:   2016-09-20 (Tue, 20 Sep 2016)

  Changed paths:
    A lib/galaxy/datatypes/converters/tabular_to_dbnsfp.py

  Log Message:
  -----------
  Merge branch 'release_16.04' into release_16.07


  Commit: 8b3356b869beba70820235c2d0894cee9e590ffe
      https://github.com/galaxyproject/galaxy/commit/8b3356b869beba70820235c2d0894cee9e590ffe
  Author: Nicola Soranzo <nicola.soranzo at tgac.ac.uk>
  Date:   2016-09-21 (Wed, 21 Sep 2016)

  Changed paths:
    M lib/galaxy/jobs/runners/slurm.py

  Log Message:
  -----------
  Strip stderr message from sacct


  Commit: 34d60e2b27ab08a3ebc5201d1c3282d346d40af0
      https://github.com/galaxyproject/galaxy/commit/34d60e2b27ab08a3ebc5201d1c3282d346d40af0
  Author: Martin Cech <cech.marten at gmail.com>
  Date:   2016-09-21 (Wed, 21 Sep 2016)

  Changed paths:
    M lib/galaxy/jobs/runners/slurm.py

  Log Message:
  -----------
  Merge pull request #2945 from nsoranzo/release_16.07_strip_stderr

[16.07] Strip stderr message from sacct


  Commit: c0e8a7608351679b8ebdb71207339384161d6616
      https://github.com/galaxyproject/galaxy/commit/c0e8a7608351679b8ebdb71207339384161d6616
  Author: Dave B <dave at bx.psu.edu>
  Date:   2016-09-22 (Thu, 22 Sep 2016)

  Changed paths:
    M lib/galaxy/webapps/tool_shed/api/repositories.py
    M lib/galaxy/webapps/tool_shed/controllers/repository.py
    M lib/galaxy/webapps/tool_shed/model/__init__.py
    M lib/tool_shed/util/metadata_util.py

  Log Message:
  -----------
  [16.07] Fix tool dependencies handling in Tool Shed model (#2950)

* Fix the cause of toolshed test 1400 failing.

* Fix handling of repositories without tool dependencies.

* Fix tool dependency retrieval.

In some cases, a process might attempt to fetch tool dependencies for revision
1:7334f6d0ac17, but the repository has been updated, and tool dependency
metadata has been reassigned to e.g. 7:ce22ceec214a. This commit resolves
that issue.

* Correct the logic that returns an empty string for an empty dict.

* Fix getting latest revision with tool dependencies.

* Use self.app instead of trans.app


  Commit: 673a9a3a5b556973741245f96fb15ccc30405da6
      https://github.com/galaxyproject/galaxy/commit/673a9a3a5b556973741245f96fb15ccc30405da6
  Author: John Chilton <jmchilton at gmail.com>
  Date:   2016-09-22 (Thu, 22 Sep 2016)

  Changed paths:
    M config/galaxy.ini.sample
    A doc/source/admin/chat-0.png
    A doc/source/admin/chat-1.png
    A doc/source/admin/chat-2.png
    A doc/source/admin/chat-3.png
    A doc/source/admin/chat-4.png
    A doc/source/admin/chat.rst
    A doc/source/admin/communication_server.png
    A doc/source/admin/communication_server_rooms.png
    A doc/source/admin/conda_faq.rst
    M doc/source/admin/index.rst
    A doc/source/releases/16.07.rst
    M doc/source/releases/16.07_announce.rst
    A doc/source/releases/16.10_announce.rst
    A lib/galaxy/datatypes/converters/tabular_to_dbnsfp.py
    M lib/galaxy/dependencies/conditional-requirements.txt
    M lib/galaxy/jobs/runners/slurm.py
    M lib/galaxy/managers/rbac_secured.py
    M lib/galaxy/tools/actions/__init__.py
    M lib/galaxy/tools/deps/__init__.py
    M lib/galaxy/tools/deps/conda_util.py
    M lib/galaxy/tools/deps/resolvers/__init__.py
    M lib/galaxy/tools/deps/resolvers/conda.py
    M lib/galaxy/tools/toolbox/base.py
    M lib/galaxy/tools/toolbox/watcher.py
    M lib/galaxy/util/template.py
    M lib/galaxy/version.py
    M lib/galaxy/webapps/galaxy/api/history_contents.py
    M lib/galaxy/webapps/tool_shed/api/repositories.py
    M lib/galaxy/webapps/tool_shed/controllers/repository.py
    M lib/galaxy/webapps/tool_shed/model/__init__.py
    M lib/tool_shed/util/metadata_util.py
    M run.sh
    M static/scripts/bundled/analysis.bundled.js
    M static/scripts/bundled/analysis.bundled.js.map
    M static/scripts/bundled/libs.bundled.js
    M static/scripts/bundled/libs.bundled.js.map
    M templates/webapps/galaxy/workflow/run.mako
    M templates/webapps/tool_shed/index.mako
    A test/functional/tools/dbkey_output_action.xml
    M test/functional/tools/samples_tool_conf.xml
    M test/unit/managers/test_DatasetManager.py

  Log Message:
  -----------
  Merge pull request #2958 from galaxyproject/release_16.07

[master-toolshed] merge in release_16.07


Compare: https://github.com/galaxyproject/galaxy/compare/3e65e768c8cb...673a9a3a5b55


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